Repetitive elements constitute nearly 50% of the human genome. Once classic examples of ''junk DNA,''Alu elements and Long Interspersed Element -1 (L1) recently gained a more prominent status as several studies established their involvement in cell functions and gene remodeling. These currently active human mobile elements are well established as significant contributors to genetic instability and associated genetic diseases, including cancer. Current estimates attribute 0.5% of human inherited genetic disorders as is having been the consequence of mobile element insertions and/or subsequent mutagenic recombination's. As all Alu copies in the human genome are generated with target site duplications that contain an L1 endonuclease recognition site, there are roughly two million potential cleavage sites adjacent to these elements that may help them contribute to Alu/Alu- mediated events. Despite the tremendous impact of Alu elements on the human genome, much of the specific aspects of the Alu elements involved in the process of Alu/Alu recombination remain unexplored. Our long-term goal is to understand why some genetic loci are particularly prone to this form of recombination and whether we can predict regions of genetic instability in the genome in order to fully assess the impact of Alu elements on human health. The objective of this application is first, to determine which factors in the Alu element influence Alu/Alu recombination rates and second, to measure Alu/Alu recombination using L1 as a source to cause double strand breaks (DSBs) both in a normal and nucleotide excision repair (NER) deficient genetic background. The central hypothesis of the application is that specific aspects of Alu elements influence in the rate of Alu/Alu recombination and that L1 endonuclease activity mediates Alu/Alu recombination in the human genome. The rationale for the proposed research is that, this series of experiments will provide us with a better understanding of the factors contributing to mutagenic recombination in the human genome, particularly among repetitive sequences. Our specific aims are: 1. To evaluate the contribution of specific aspects of the Alu elements to non-allelic homologous recombination. We will specifically evaluate the importance of orientation (direct repeats, inverted repeats), mismatch, A-tail length, and distance between these repetitive elements. 2. To determine the role of L1 endonuclease activity in Alu/Alu recombination in normal and NER deficient genetic backgrounds. PUBLIC HEALTH RELEVANCE: The currently active human mobile elements families (Line 1 and Alu) are well established as significant contributors to genetic instability and associated genetic diseases, including cancer. This proposal will provide us with a better understanding of the factors contributing to mutagenic recombination in the human genome, particularly among repetitive sequences. Ultimately, the results of our research could allow us to figure out a number of rules that allow predictions about the stability of various genomic regions based on Alu/Alu recombination potential.